readGATK: Read in input vcf data in GATK format for Contamination...
In sssc: Same Species Sample Contamination Detection
Description
Usage
Arguments
Value
Description
Read in input vcf data in GATK format for Contamination detection
Usage
1
readGATK(dr, dbOnly, depCut, thred, content, extnum, keepall)
Arguments
dr
A valid input object
dbOnly
Use dbSNP as filter, default is FALSE, passed from read_vcf
depCut
Use a threshold for min depth , default is False
thred
Threshold for min depth, default is 20
content
Column names in VCF files
extnum
The column number or numbers to be extracted from vcf, default is 10; 0 for not extracting any columns
keepall
Keep unextracted column in output, default is TRUE, passed from read_vcf
Value
Dataframe from VCF file
sssc documentation built on May 2, 2019, 4:03 p.m.
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Description Usage Arguments Value
Description
Read in input vcf data in GATK format for Contamination detection
Usage
1 | readGATK(dr, dbOnly, depCut, thred, content, extnum, keepall)
|
Arguments
dr |
A valid input object |
dbOnly |
Use dbSNP as filter, default is FALSE, passed from read_vcf |
depCut |
Use a threshold for min depth , default is False |
thred |
Threshold for min depth, default is 20 |
content |
Column names in VCF files |
extnum |
The column number or numbers to be extracted from vcf, default is 10; 0 for not extracting any columns |
keepall |
Keep unextracted column in output, default is TRUE, passed from read_vcf |
Value
Dataframe from VCF file
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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